Contacts of the strand formed by residues 205 - 210 (chain A) in PDB entry 1W3U
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 205 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU 3.6 0.3 - - - +
72A PHE* 3.5 4.5 - - - -
73A ILE* 2.7 49.0 + - - +
74A GLN 5.0 0.7 - - - -
76A GLY* 3.0 48.3 + - - +
77A ALA* 3.8 1.5 + - - +
80A GLN* 3.9 20.9 - - + -
193A ALA 3.4 23.8 - - - +
194A GLY* 4.2 1.4 - - - -
204A VAL* 1.3 76.1 + - - +
206A VAL* 1.3 68.4 + - - +
207A VAL* 3.7 3.4 + - + -
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 3.7 25.8 - - + -
70A VAL* 4.4 4.0 - - + -
71A LEU 3.6 7.2 - - - +
72A PHE* 4.2 19.3 - - + -
178A ILE* 4.8 6.7 - - + -
192A TYR* 3.1 5.4 - - - +
193A ALA* 2.8 42.2 + - + +
195A ALA* 5.0 4.3 - - + -
199A LEU* 3.7 26.5 - - + -
204A VAL* 4.1 5.1 - - + -
205A THR* 1.3 71.6 - - - +
207A VAL* 1.3 64.2 + - - +
208A ILE* 3.9 20.2 - - + -
248A VAL* 4.9 6.3 - - + -
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Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LYS 3.6 1.4 - - - +
70A VAL* 3.7 0.3 - - - -
71A LEU* 2.7 50.9 + - + +
73A ILE* 3.7 22.0 - - + -
80A GLN* 3.6 33.2 - - + +
190A LEU* 3.9 33.9 - - + -
191A VAL 3.4 4.3 - - - +
192A TYR* 4.1 2.7 - - + -
205A THR* 4.2 5.4 - - + +
206A VAL* 1.3 78.8 - - - +
208A ILE* 1.3 63.0 + - - +
209A VAL* 4.6 0.9 - - + -
227A TYR* 4.0 12.3 - - + -
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Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 3.5 29.6 - - + -
59A LEU* 4.4 2.0 - - + -
62A LEU* 4.0 13.9 - - + -
68A TYR* 4.2 11.7 - - + -
69A LYS 3.4 9.2 - - - +
70A VAL* 4.3 16.4 - - + -
178A ILE* 4.4 7.6 - - + -
185A LEU* 3.6 28.1 - - + +
189A GLY 4.6 0.2 - - - -
190A LEU* 3.2 3.6 - - - +
191A VAL* 2.8 58.1 + - + +
206A VAL* 3.9 16.4 - - + -
207A VAL* 1.3 75.8 - - - +
209A VAL* 1.3 62.1 + - - +
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TYR* 3.4 5.6 - - - -
69A LYS* 2.9 43.0 + - + +
71A LEU* 3.8 23.8 - - + -
88A PHE* 4.6 2.7 - - + -
189A GLY 3.5 10.3 - - - +
190A LEU* 4.0 21.8 - - + -
207A VAL* 4.6 3.1 - - + -
208A ILE* 1.3 76.1 - - - +
210A ARG* 1.3 76.3 - - - +
211A GLU* 3.3 1.1 + - - +
213A LEU* 4.9 1.1 - - + -
214A VAL* 3.7 37.0 - - + -
227A TYR* 5.3 0.9 - - + -
231A VAL* 4.4 6.1 - - + -
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Residues in contact with ARG 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A GLY* 3.6 9.2 - - - +
68A TYR* 2.9 40.5 + - + -
169A PRO* 6.0 2.0 - - - +
186A ASN* 3.2 27.1 + - - +
187A GLN 4.2 2.8 + - - -
188A PHE 3.1 23.8 + - - +
189A GLY* 2.8 24.3 + - - +
209A VAL* 1.3 74.8 - - - +
211A GLU* 1.3 61.6 + - - +
212A ASP* 2.8 35.4 - - - +
213A LEU* 2.9 38.2 + - + +
214A VAL 3.8 1.0 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il